A method and system for multi-part left atrium (LA) segmentation in a C-arm CT volume is disclosed. Multiple LA part models, including an LA chamber body mesh, an appendage mesh, a left inferior pulmonary vein (PV) mesh, a left superior PV mesh, a right inferior PV mesh, and a right superior PV mesh, are segmented in a 3D volume. A volume mask is generated from the LA chamber mesh, the appendage mesh, and the PV meshes. Erosion is performed in the LA chamber body and a plurality of ostia regions in the volume mask. The plurality of ostia regions in the volume mask are refined using region growing, and a smooth mesh is fit to each ostia region. A consolidated LA mesh is generated from the volume mask and the parts of the LA mesh are relabeled in the ostia region based on part boundaries detected using an optimization approach.